Maybe this is proof that the melachos come from the day-to-day operation of the Mishkan rather than construction. I believe R. Ribiat, in his magisterial 39 Melachos, writes that they would light the wicks of the menora and then extinguish them in order to properly prep them for the real lighting.
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TzviFeb 16 '11 at 14:33

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I wonder whether that's so, though. After all, one of the things done day-to-day in the Mishkan was dissecting animals brought as korbanos; but that sort of cutting is not a melachah (see Orach Chaim 324:7, which permits cutting up a dead animal for dog food if it's too tough for them to eat otherwise).
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AlexFeb 16 '11 at 19:05

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Rashi (Shabbos 73a, ד"ה מכבה) says that it was done when boiling the herbs to make the various dyes. (If the fire was burning too hot, they'd have to partially extinguish it so the dye wouldn't be ruined.)

However, Tosafos (Shabbos 94a, ד"ה ר' שמעון) argue that the artisans would have been careful to make the fire the right size to begin with. They say instead, as Shalom wrote, that extinguishing a fire was done in order to produce charcoal for metalworking.

My understanding -- and someone please correct me if I'm getting this wrong -- is that for the metalworking they needed to do, an ordinary wood fire didn't burn hot enough.

The alternative was something known to ancient societies, that if you take a pile of wood, cover it with clay so no oxygen can get in, and then burn it, instead of "burning" (oxidation) into ash, it pyrolizes into charcoal. You then put this fire out, and light up your charcoal for metal-working; it burns much hotter than a wood fire, and enables a lot more things to be done with metal. So that initial "extinguishing" was constructive towards an end-goal, not just "eh we don't need the fire anymore."

this is evident from the mishnah in second chapter of shabbat which says that if you extinguish a candle you have transgressed because it creates pekham ash or coals. It is also described as the process called "hivhuv" they would spin the wicks and then cinge the tip to enable easier lighting (mishna shabbat chapter 2)
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Eytan YammerMar 18 '12 at 15:19